I wanted to run a python script main.py multiple times with different arguments through a sbatch_run.sh script as in:
#!/bin/bash
#SBATCH --job-name=sbatch_run
#SBATCH --array=1-1000
#SBATCH --exclude=node047
arg1=10 #arg to be change during runs
arg2=12 #arg to be change during runs
python main.py $arg1 $arg2
The arguments are encoded in the bash file ran by sbatch. I was worried that if I ran sbatch_run.sh multiple times one after the other but changing the value of arg1 and arg2 during each run, that it might cause errors in my runs. For example if I do:
sbatch sbatch_run.sh # with arg1=10 and arg2=12
and then immediately after I change sbatch_run.sh but run the file again as in:
sbatch sbatch_run.sh # with arg1=69 and arg2=666
would case my runs to all run with the last one (i.e. arg1=69 and arg2=666) instead of each run with its own arguments.
I know for sure that if I hard code the arguments in main.py and then run the same sbatch script but change the main.py it will run the last one. I was wondering if that is the case too if I change the sbatch_run.sh script.
Just so you know, I did try this experiment, by running 1000 scripts, then some get queued and put a sleep command and then change the sbatch_run.sh. It seems to not change what my run is, however, if I am wrong this is way too important to be wrong by accident and wanted to make sure I asked too.
For the record I ran:
#!/bin/bash
#SBATCH --job-name=ECHO
#SBATCH --array=1-1000
#SBATCH --exclude=node047
sleep 15
echo helloworld
echo 5
and then change the echo to echo 10 or echo byebyeworld.
When sbatch is run, Slurm copies the submission script to its internal database ; you can convince yourself with the following experiment:
$ cat submit.sh
#!/bin/bash
#SBATCH --hold
echo helloworld
The --hold is there to make sure the job does not start. Submit it :
$ sbatch submit.sh
Then modify the submission script:
$ sed -i 's/hello/bye/' submit.sh
$ cat submit.sh
#!/bin/bash
#SBATCH --hold
echo byeworld
and now use control show job to see the script Slurm is planning to run:
$ scontrol show -ddd job YOURJOBID
JobId=******* JobName=submit.sh
[...]
BatchScript=
#!/bin/bash
#SBATCH --hold
echo helloworld
[...]
It hasn't changed although the original script has.
[EDIT] Recent versions of Slurm use scontrol write batch_script <job_id> [<optional_filename>] rather than scontrol show -dd job to write the submission script to a file named <optional_filename>. The optional filename can be - to display the script to the screen rather than save it to a file.